Weary Soul of Ikari Shinji
by Trek1030
Summary: After Ritsuko destroys the Rei clones, there is one more room Misato and Shinji must see. But this room, and the secrets within, will further destroy all Shinji knows, and leave him wondering why?


The Weary Soul of Ikari Shinji

Chapter 1: Discovery

* * *

Dr. Akagi Ritsuko walked calmly down an eerily dark corridor, followed closely by Major Katsuragi Misato accompanied by the young Ikari Shinji. The trio had just left a cloning lab with a storage tank filled with disintegrating human-looking body parts. The Major felt torn to pieces, especially after what she had just witnessed, and what she had just learned; everything seemed much different now. Ritsuko used to be her friend, and perhaps she still was, but what should she be considered now? Dr. Akagi had destroyed a tank full of Ayanami clones, and then broke down crying about her affairs with Commander Ikari, finishing off with words of hatred toward herself.

"Please tell me that this sick tour is over," pleaded Shinji. He stood with his head hung low, his face hidden; though his emotions could be seen through the sad tone in his voice and by the quick breaths he inhaled, indicating his soft crying.

"Yes Shinji. Let's go home." Misato replied, her voice sounding monotone, but forced. Within, she forced herself to keep her composure until she could reach her apartment, a safe heaven where she would later drown her nightmare reality with an ocean of Yebisu. The Major looked over to Ritsuko, who was silently standing slightly in front of her in the hallway. "Come on, let's get out of here."

"Wait Misato," the Doctor said, sounding broken in her spirits, "There's one more room for you to see."

"I've already seen where that Angel is kept," Misato responded, "It's Adam or Lilith or whatever the hell it's called. Like I said, let's get going."

"No, that's not it. I… I just can't tell you. You have to see it; besides, this most definitely concerns Shinji. And I don't think that he's going to want to come back here, but this is the only way he's going to learn the truth."

Shinji looked up at the Doctor. His eyes were red from crying, and he looked thoroughly worn out from the night's discoveries. He spoke, quietly and slowly. "I'm not ever going down to where ever we are again. But I want to know the truth, all of it; I hate NERV, but it's taken my life away from me, and I want to know just why. So, Misato, let's follow her if it brings us closer to knowing the truth."

Misato nodded in agreement, and she and Shinji followed Ritsuko further down the hall. Their soft footsteps echoed through the empty corridor, until they eventually arrived at their destination: a metal door, dimly illuminated by a single fluorescent light mounted to the wall above the door. After Ritsuko quickly entered a sequence into the keypad next to the door, the massive gate of metal retracted into the sidewalls, leaving a gateway open into the darkness of the odd room before the trio.

Misato and Shinji walked cautiously into the room, trailing behind Dr. Akagi, who had already stopped at a computer terminal. After a long silence only broken by the tapping of keys and the chirp of computer responses, dim blue lights on the floor along the base of the walls lit up the room. Surrounding the three NERV personnel was the shimmering and haunting cloning LCL from within a massive empty tank. The yellow color of the LCL blended with the glowing blue lights, producing a putrid green light along the sides of the room. The sickening green light reflected off of a metal cylinder in the center of the room, which extended from the ceiling into the floor. The metal cylinder seemed as though it could move, as warnings and arrows and such were plastered around the exterior.

"This is another cloning lab?" Misato stated, momentarily closing her eyes as the thought scared her. She reached into her jacket and unsheathed her semi-automatic pistol, raising it for the second time this evening at the doctor who had once been her friend. "Take us out of here, Ritsuko. Shinji and I don't want to witness again the hell that we've learned about; that includes watching you dismember the remaining Ayanami clones."

"Put your gun away Misato," Ritsuko pleaded, "There are no more Ayanami clones left. Yes, this place is a cloning lab. But inside that cylinder, rests another truth that you and Shinji must know." She limply pointed to the metal container in the center of the room.

"Alright," Misato coldly replied, after thinking it over a second. She holstered her gun, then crossed her arms, standing there waiting for what she was to be shown. The Major watched as Ritsuko turned once more to the computer and began something. Misato began to notice a pressure on her arm; looking down, she realized it was Shinji holding onto her like a scared child. Unconsciously, he desperately sought something, anything, to cling to, his fragile mind nearly shattered after truths he learned and life he lived; the anticipation of one more truth, perhaps the most devastating one, drove him to seek someone to help him through this.

"Okay," Ritsuko started, turning to face the two, "I'll explain. This room we are in is another cloning lab. These tanks," she lifted her arm to point around, "are cloning storage tanks, just like the one in the other lab. Obviously, these tanks are empty," she paused allowing herself a disturbing giggle, "that is because all the spares that this tank held, have been used up."

"But Ritsuko-san," Shinji stuttered, "how… how can that be? Rei… she hasn't died many times? Has she?"

"No," Ritsuko said, laughing a tiny bit more. She knew she would disrupt the commander's plans with this, perhaps even destroy the one last person Gendo should care about; maybe even cause him some grief, even if it's just momentary. With these thoughts in mind, Ritsuko smiled and spoke again. "No, of course not, Shinji. Rei has only died twice so far. But these tanks never held any clones of hers."

"Then what the hell else have you been cloning?" Misato yelled, feelings of fear beginning to grow. "What the hell was in these tanks? And what the hell is in that tube?"

"Well, Misato," Ritsuko said, her deranged smile still beaming, "the storage tanks held clones of some one important, and original is still here, albeit he's dead. That is what is in the tube. The reasons we've taken great care that he continue to survive after death is that without this person, there would be no Eva Project and Instrumentality could not take place."

"Who is it?" Shinji suddenly piped up, hoping that in some strange way, maybe it was his father that was behind the cylinder. His real father, not the cold bastard everyone called the Commander. Yes, ideas rapidly forming in his head, Shinji hoped that his father had died, and his corpse was now floating in that tube; and that the nightmare that had started when he came to Tokyo-3 was because of a clone, and that maybe Shinji could find peace in that and perhaps forgive his father's tortured soul. Was that the truth at needed to be known? So the young boy asked once more, "Whose body is in the tube?"

Ritsuko turned back to the computer terminal, and quickly typed in a command. Slowly, the metal cylinder in the center of the room began to part: splitting in the middle, with the halves retracting into the floor and ceiling. Behind the metal façade, a glass tube was revealed, exposing a dimly lighted body floating in the LCL. The body floated there unmoving, showing off its wounds inflicted during its last living hours. One arm was bent at strange angle because of the long wound that snaked down it, and the serrated bone that stuck out from when it was wrenched apart by a beast. That same beast had caused the other deadly injuries in the body. The LCL preserved the body from decomposition, though it did not absorb the blood that floated in it, which had come from the open wounds on the corpse. A hazy red cloud in the LCL somewhat floated around the head, a massive cranial injury its rupturing point. Almost the entire right hemisphere of the corpse's skull seemed to have been blasted away; a gaping hole with remnants of brain matter and a single floating eyeball resides where the right half of the body's face should have been. Through all this damage, the other half of the face was unscathed, perfectly preserved in LCL, with a single good eyeball still in its socket staring back at whoever gazed at these remains. That eyeball gazed back Shinji and Misato, who stared with wide eyes in recognition of who was floating in the tube.

Misato went limp, nearly fainting as Shinji let go of her arm. She looked back at the tube and screamed a scream that would echo throughout NERV. Misato restrained her emotions to no more, sobbing as she gazed at what was before her.

Shinji stared at the body in the tube while he fell to his knees. He hung his head down as he closed his eyes and began to cry; in his confusion he pounded and the floor until fist was bruised. Still crying, the distraught pilot looked up at Dr. Akagi, who had since stood with her eyes closed, a small smile on her face. He asked her one question, one simple yet complex question, which she would soon answer for him.

"Why am I in that tube?"

The corpse of the first Ikari Shinji just stared silently at the scene from behind its glass resting place. His cold, never blinking eyes forever trapped in an expression of pain; a pain so terrible that the only possible release was death. But it was not to be. NERV dragged down his soul from eternal peace.

Because they had a use for him.

* * *

Shinji and Misato sat at their kitchen table. Several days had passed since that horrid night Ritsuko revealed NERV's secrets to them and there had only been silence between the NERV officer and her ward. Thoughts and guilt pounded through Misato's head as she sat there and looked at the boy in front of her. Shinji sat hunched over, his head down, unable to look at any other person in the face. With his head still down, Shinji broke the prevailing silence.

"Why," he asked softly, nearly a whisper, "did you want to speak to me Misato?"

"You've been hiding in your room since that night," Misato answered gently, "and I've been hiding from you. I know that you've needed me, and I haven't been there. We need to talk, Shinji… about that night."

Shinji remained silent, his thoughts a mess. The very foundation of his being was shaken when he saw himself in that tube. So many questions assaulted his mind, so many things he needed to know.

"Just…" he began, hesitating slightly, "I just want to know… why… why couldn't they let me die…"

"Don't think like that!" Misato responded sharply, "You're here, you're alive!"

"Am I really? Am I really human, Misato?!" the boy shouted angrily, "I've died before. And yet I'm here. Normal people don't do that! Do I even have a soul anymore?! When did I lose it…"

"Shinji…" the older woman tried to soothe him, but was interrupted.

"You can't stand to be around me, can you!" he screamed, slowing beginning to sob, "That's why… why when I needed you… you weren't there… why Asuka's gone… why Ayanami had to die… why I'm all alone… it's some kind of punishment, isn't it? For being this… this thing…."

"No…" Misato cooed, reaching over to place her hands over his, "That's not right Shinji… it's not your fault… it never was your fault."

"I shouldn't be alive…"

* * *

Later that night, Ikari Shinji came to an important decision. Despite the pain he was in, despite the feeling of loss that threatened to drown him, he would go on. But only for one reason: knowledge. He resolved that night to find out why this had happened to him, how he had died, how many times he had died.

_Perhaps then,_ the boy thought, _I'll finally know peace._

**To be continued…**

Notes:

Found this story while going through some very old files. Decided to clean it up and continue it, since I have a lot of free time suddenly. Expect short chapters (like this one), morbid humor, and angst abound.


End file.
